Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea.
Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia; Max Rubner-Institut, Federal Research Institute of Nutrition and Food, 95326 Kulmbach, Germany.
Int J Biol Macromol. 2022 May 31;208:381-389. doi: 10.1016/j.ijbiomac.2022.03.115. Epub 2022 Mar 23.
Type I restriction-modification enzymes are oligomeric proteins composed of methylation (M), DNA sequence-recognition (S), and restriction (R) subunits. The different bipartite DNA sequences of 2-4 consecutive bases are recognized by two discerned target recognition domains (TRDs) located at the two-helix bundle of the two conserved regions (CRs). Two M-subunits and a single S-subunit form an oligomeric protein that functions as a methyltransferase (MS MTase). Here, we present the crystal structure of the intact MTase from Vibrio vulnificus YJ016 in complex with the DNA-mimicking Ocr protein and the S-adenosyl-L-homocysteine (SAH). This MTase includes the M-domain with a helix tail (M-tail helix) and the S-domain of a TRD and a CR α-helix. The Ocr binds to the cleft of the TRD surface and SAH is located in the pocket within the M-domain. The solution- and negative-staining electron microscopy-based reconstructed (MS) structure reveals a symmetric (S) assembly using two CR-helices and two M-tail helices as a pivot, which is plausible for recognizing two DNA regions of same sequence. The conformational flexibility of the minimal MS MTase dimer indicates a particular state resembling the structure of MS MTases.
I 型限制修饰酶是由甲基化（M）、DNA 序列识别（S）和限制（R）亚基组成的寡聚蛋白。由两个可区分的靶标识别结构域（TRD）位于两个保守区（CR）的双螺旋束上，识别出 2-4 个连续碱基的不同二聚体 DNA 序列。两个 M 亚基和一个 S 亚基形成一个寡聚蛋白，作为甲基转移酶（MS MTase）发挥作用。在这里，我们展示了完整的 MTase 从创伤弧菌 YJ016 与 DNA 模拟 Ocr 蛋白和 S-腺苷-L-同型半胱氨酸（SAH）复合物的晶体结构。该 MTase 包括 M 结构域和 TRD 的 S 结构域和 CR α-螺旋。Ocr 结合到 TRD 表面的裂隙中，SAH 位于 M 结构域内的口袋中。基于溶液和负染色电子显微镜重建（MS）结构揭示了使用两个 CR 螺旋和两个 M 尾螺旋作为枢轴的对称（S）组装，这可能是识别两个相同序列 DNA 区域的原因。最小的 MS MTase 二聚体的构象灵活性表明了一种特殊的状态，类似于 MS MTase 的结构。
